{
  "abstract": "Cryo-electron tomography provides unique insights into macromolecular complexes in their native environments, yet membrane analysis remains a major bottleneck due to low signal-to-noise ratios, missing wedge artifacts and the complexity of membrane-associated particles. Existing tools often require extensive manual annotation, struggle with generalization across datasets and lack integrated solutions for segmentation, particle localization and quantitative analysis. We introduce MemBrain v2, a deep-learning-enabled framework that unifies these tasks into a streamlined pipeline. MemBrain-seg leverages a diverse, collaboratively generated training dataset and specialized model training strategies to achieve generalizable membrane segmentation across variable tomographic conditions. MemBrain-pick enables data-efficient localization of membrane-bound particles by integrating geometric constraints with deep learning, reducing the need for extensive manual annotation. MemBrain-stats provides quantitative insights into particle distributions, computing spatial metrics to analyze intramembrane particle organization. MemBrain v2 integrates seamlessly into cryo-electron tomography workflows, providing an accessible and structured approach to membrane analysis.",
  "abstract_shown": true,
  "affiliations": [
    "Biozentrum, University of Basel, Basel, Switzerland. lorenz.lamm@tum.de",
    "Helmholtz Munich, German Research Center for Environment and Health, Munich, Germany. lorenz.lamm@tum.de",
    "School of Computation, Information and Technology, Technical University of Munich, Munich, Germany. lorenz.lamm@tum.de",
    "Biozentrum, University of Basel, Basel, Switzerland",
    "Helmholtz Munich – German Research Center for Environment and Health, Munich, Germany",
    "School of Computation, Information and Technology, Technical University of Munich, Munich, Germany",
    "Helmholtz Munich, German Research Center for Environment and Health, Munich, Germany",
    "Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland",
    "Swiss Institute of Bioinformatics, Basel, Switzerland",
    "MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK",
    "Department of Structural Biology, Genentech, South San Francisco, CA, USA",
    "MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK",
    "Department of Information and Communications Engineering, Faculty of Computers Sciences, University of Murcia, Murcia, Spain",
    "German Cancer Research Center (DKFZ), Division of Medical Image Computing, Heidelberg, Germany",
    "Helmholtz Imaging, German Cancer Research Center (DKFZ), Heidelberg, Germany",
    "School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK",
    "Munich Center for Machine Learning, Munich, Germany",
    "Biozentrum, University of Basel, Basel, Switzerland. ben.engel@unibas.ch",
    "Helmholtz Munich, German Research Center for Environment and Health, Munich, Germany. tingying.peng@helmholtz-munich.de",
    "School of Computation, Information and Technology, Technical University of Munich, Munich, Germany. tingying.peng@helmholtz-munich.de"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 15,
  "authors": [
    {
      "affs": [
        0,
        1,
        2,
        3,
        4,
        5
      ],
      "name": "Lorenz Lamm",
      "orcid": "0000-0003-0698-7769"
    },
    {
      "affs": [
        3
      ],
      "name": "Simon Zufferey",
      "orcid": "0009-0005-5483-4566"
    },
    {
      "affs": [
        6,
        5,
        3
      ],
      "name": "Hanyi Zhang",
      "orcid": "0009-0001-6314-9158"
    },
    {
      "affs": [
        3
      ],
      "name": "Ricardo Diogo Righetto",
      "orcid": "0000-0003-4247-4303"
    },
    {
      "affs": [
        3,
        7,
        8
      ],
      "name": "Florent Waltz",
      "orcid": "0000-0002-2251-3363"
    },
    {
      "affs": [
        3,
        9
      ],
      "name": "Wojciech Wietrzyñski",
      "orcid": "0000-0001-8898-2392"
    },
    {
      "affs": [
        7,
        8,
        4,
        5
      ],
      "name": "Kevin A. Yamauchi",
      "orcid": "0000-0002-7818-1388"
    },
    {
      "affs": [
        10,
        11,
        4,
        5
      ],
      "name": "Alister Burt",
      "orcid": "0000-0002-9341-2295"
    },
    {
      "affs": [
        6,
        5,
        12
      ],
      "name": "Ye Liu",
      "orcid": "0000-0002-1901-669X"
    },
    {
      "affs": [
        12,
        13,
        14
      ],
      "name": "Antonio Martínez-Sánchez",
      "orcid": "0000-0002-5865-2138"
    },
    {
      "affs": [
        13,
        14
      ],
      "name": "Sebastian Ziegler",
      "orcid": "0000-0002-1693-5586"
    },
    {
      "affs": [
        13,
        14,
        4,
        15,
        5
      ],
      "name": "Fabian Isensee",
      "orcid": "0000-0002-3519-5886"
    },
    {
      "affs": [
        6,
        16,
        15,
        5,
        3
      ],
      "name": "Julia A. Schnabel",
      "orcid": "0000-0001-6107-3009"
    },
    {
      "affs": [
        17,
        4,
        5
      ],
      "name": "Benjamin D. Engel",
      "orcid": "0000-0002-0941-4387"
    },
    {
      "affs": [
        18,
        19
      ],
      "name": "Tingying Peng",
      "orcid": "0000-0002-7881-1749"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/3y0jk1bbkkk1s.bib",
  "cited_by": 179,
  "doi": "10.1038/s41592-026-03178-8",
  "fulltext_url": null,
  "id": "3y0jk1bbkkk1s",
  "issns": [
    "1548-7091",
    "1548-7105"
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  "landing_url": "https://doi.org/10.1038/s41592-026-03178-8",
  "language": "en",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
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      "openalex",
      "1315|Advanced Electron Microscopy Techniques and Applications"
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  "openalex": "W4390782971",
  "pdf_url": null,
  "pmcid": null,
  "pmid": "42711494",
  "published": "2026-09-08",
  "publisher": "Nature Portfolio",
  "ris": "https://research.draconitic.com/paper/3y0jk1bbkkk1s.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T13:26:46Z",
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      "url": "https://doi.org/10.1038/s41592-026-03178-8"
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  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1315|Advanced Electron Microscopy Techniques and Applications",
      "subfield": "structural-biology"
    }
  ],
  "title": "MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography",
  "title_text": "MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography",
  "type": "peer-reviewed",
  "updated_at": "2026-11-09T13:21:05Z",
  "url": "https://research.draconitic.com/paper/3y0jk1bbkkk1s",
  "venue": "Nature Methods",
  "versions": []
}